This study compared the nanoleakage of retrograde filling with calcium silicate-based putty and mineral trioxide aggregate by using traditional and lid techniques. Sixty extracted human teeth were instrumented for retrograde filling and divided into four groups according to the retrograde filling technique. Teeth in each group were filled with different material combinations. Nanoleakage was evaluated twice on days 1, 3, 7, 15, and 30 at the nanoscale level (nL/s). Kruskal–Wallis and Mann–Whitney U-tests were used. The Well-Root, Ceraseal + Well-Root, and Ceraseal + ProRoot groups showed less nanoleakage than the ProRoot group in the first week (P < .05). Although the groups did not show significant differences after 2 weeks, the Ceraseal + ProRoot group showed less leakage than ProRoot group on days 3 and 7 (P < .05). Scanning electron microscopy showed good adaptation. Filling with a calcium silicate-based putty alone and the lid technique was faster with less nanoleakage compared to mineral trioxide aggregate.